Expression Profiling Of Aneuploidy Genome In Rice

Aneuploidy involves changes in chromosomal copy number compared with normal euploid genotypes. Aneuploidy causes severe developmental defects and is a condition frequently found in tumor cells. Aneuploidy genome is in the state of unbalance, which affects the global genome transcriptional and epigenetic regulation. Aneuploidy gene expression in a variety of species have claimed many different types of responses. Individual duplicated genes suggest that there are both structural gene dosage effects and compensation in aneuploids. It has been found that the common types of aneuploid are monomer (2n-1), nullisomic (2n-2), trisomy (2n+1), tetrasome (2n+2) and so on. In this study, using next generation transcriptomics sequencing technology (RNA-seq), we profiled the transcriptomes of two rice aneuploid trisomy 1 and trisomy 11. We obtained the following results:1. T1 had the following traits:grassy, long and narrow leaves, pale, loose plant type, more tillers, hook shaped grain terminal, less number of grains per panicle and low setting rate. The traits were top spikelet degradation, tillering, and very pale leaves color in T11. Two trisomics demonstrated a strong decline in the rate of setting, light leaf color washout characteristics.2. Illumina Hiseq2500 sequencing platform required for the study of mRNA sequencing, Tophat and Cufflinks required for data analysis. A total of 4G (50-bp) reads were obtained from each sample, and over 40278 mRNAs were identified by gene annotation. Distribution of reads on the genome is consistent.75.4% reads mapped to the transcription of exon region,3.1% is intron regions.3. We used the FPKM to evaluate the gene expression level. Global analysis of gene expression profiles and functional analysis of differentially expressed (DE) genes were implemented. Compared to the expressed genes number in normal euploid,582(1.70%) and 990(2.83%) DE genes are determined in T1 and T11 respectively.180 DE genes are overlapped in both of T1 and T11.4. In T1,96.89% genes from chromosome 1 showed a compensation effect, while only 2.85% showed a gene dosage effect for up-regulated genes and 0.26% showed the ratio of inverse dosage effects. In T11, up-regulated genes was 3.62%, down regulated genes was 0.22%. The results show that the dosage effect and dosage compensation coexisted in aneuploidy genome, however most genes showed compensation effect.5. In T1 and T11, the differentially expressed genes on another chromosomes had a ratio of 0.7%-1.5% and 1.5% ～2.5%, respectively. The differences was not significant between the different chromosomes, which show that the additional chromosome had an impact on genome-wide expression.6. GO enrichment analysis and KEGG pathway enrichment analysis of differentially expressed in different trisomy genomes were conducted. Genes that were involved in the response to stress were consistently up-regulated, and genes associated with the cell cycle and cell proliferation were down-regulated in aneuploidy cells. Different aneuploidies induced similar changes in gene expression, independent of the specific chromosomal aberrations. Under the influence of the trisomys, differentially expressed genes involved in many biological processes, including acetaldehyde acid metabolism, photosynthesis, and pentose phosphate metabolism.